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Bioinformatics pipeline summary

Where we see the pipeline processes

Author: Adrien Taudière

Date: December 3, 2024

Summary of the bioinformatic pipeline

Code 
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/01_bioinformatics.qmd")
source(here::here("R/styles.R"))
source(here::here("R/functions.R"))

Timeline and cpu usage

Code 
log_data <- autometric::log_read(
  here::here("data/data_final/autometric_log.txt"),
  units_time = "hours",
  units_memory = "gigabytes"
)

log_data |>
  filter(!grepl("conclude:", phase)) |>
  filter(!grepl("prepare:", phase)) |>
  filter(!grepl("__DEFAULT__", phase)) |>
  ggplot(aes(x = time, y = reorder(phase, desc(time)), color = resident)) +
  geom_line(aes(linewidth = cpu)) +
  scale_color_viridis_b("Memory (Gb)", end = 0.9, direction = -1) +
  theme_idest() +
  xlab("Time (in hours)") +
  ylab("")

Main phyloseq object

You may want to select another targets such as d_asv or d_vs_mumu for example.

Code 
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
Cleaning suppress 0 taxa and 26 samples.
Code 
summary_plot_pq(d_pq)
Cleaning suppress 0 taxa and 0 samples.

Code 
tar_glimpse(script=here::here("_targets.R"), targets_only = TRUE, callr_arguments = list(show = FALSE))
Code 
tar_meta(store=here::here("_targets/"), targets_only = TRUE) |> 
  dplyr::mutate(time = paste0(seconds %/% 3600,":",seconds %/% 60,":",floor(seconds %% 60)))|>
  dplyr::select(name, seconds, bytes, format, time) |>
  dplyr::mutate(Gb=round(bytes/10^9,2)) |>
  dplyr::arrange(desc(seconds), desc(bytes))  |> 
  kable()
name seconds bytes format time Gb
d_asv 15175.810 1121258 rds 4:252:55 0.00
tax_tab 5874.178 810117 rds 1:97:54 0.00
ddF 1706.088 134739992 qs 0:28:26 0.13
ddR 1416.051 146350364 qs 0:23:36 0.15
filtered 642.999 166 rds 0:10:42 0.00
quality_raw_seq 577.204 19103 rds 0:9:37 0.00
quality_seq_wo_primers 502.534 18972 rds 0:8:22 0.00
cutadapt 325.437 69632 file 0:5:25 0.00
quality_seq_filtered_trimmed_FW 255.565 11354 rds 0:4:15 0.00
quality_seq_filtered_trimmed_REV 255.029 11354 rds 0:4:15 0.00
err_fs 241.244 21768 qs 0:4:1 0.00
err_rs 231.799 24521 qs 0:3:51 0.00
derep_rs 211.368 2780860228 qs 0:3:31 2.78
derep_fs 183.569 1764068735 qs 0:3:3 1.76
track_sequences_samples_clusters 112.782 422 rds 0:1:52 0.00
merged_seq 101.611 1440062 qs 0:1:41 0.00
track_by_samples 94.841 9016 rds 0:1:34 0.00
bioinfo_report 47.120 44 rds 0:0:47 0.00
seqtab_wo_chimera 15.211 818071 rds 0:0:15 0.00
d_vs 5.692 918040 rds 0:0:5 0.00
d_vs_mumu 4.358 902295 rds 0:0:4 0.00
d_vs_mumu_rarefy 0.349 868910 rds 0:0:0 0.00
seq_tab_Pairs 0.259 960195 rds 0:0:0 0.00
data_phyloseq 0.091 1039190 rds 0:0:0 0.00
s_d 0.045 10846 rds 0:0:0 0.00
seqtab 0.011 811557 rds 0:0:0 0.00
asv_tab 0.011 811434 rds 0:0:0 0.00
data_raw 0.010 5380 rds 0:0:0 0.00
sam_tab 0.004 3577 rds 0:0:0 0.00
fastq_files_folder 0.002 45056 file 0:0:0 0.00
file_sam_data_csv 0.001 3858 file 0:0:0 0.00
data_fnfs 0.001 2763 rds 0:0:0 0.00
samp_n_otu_table 0.001 1996 rds 0:0:0 0.00
file_refseq_taxo 0.000 114270891 file 0:0:0 0.11
data_fnrs 0.000 2763 rds 0:0:0 0.00

Load phyloseq object from targets store

Code 
d_pq <- tar_read("d_vs", store=here::here("_targets/"))

The {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.

The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.

Sample data

Code 
DT::datatable(d_pq@sam_data)

Sequences, samples and clusters across the pipeline

Code 
kable(tar_read(track_sequences_samples_clusters, store=here::here("_targets/")))
nb_sequences nb_clusters nb_samples
Raw Forward sequences 18499235 NA 376
Forward wo primers 15727443 NA 376
Forward sequences 14291477 29893 360
Paired sequences 9954646 12434 360
Paired sequences without chimera 9634094 10441 360
Paired sequences without chimera and longer than 200bp 9599091 10281 360
ASV denoising 9599091 10281 360
OTU after vsearch reclustering at 97% 9599091 4521 360
OTU vs after mumu cleaning algorithm 9599091 4160 334
OTU vs + mumu + rarefaction by sequencing depth 594000 3522 297
Code 
tab_samp <- tar_read(track_by_samples, store=here::here("_targets/"))

for (li in names(tab_samp)) {
  print(knitr::kable(tab_samp[[li]], caption = li, format="html"))
  cat('\n<!-- -->\n\n')
}
samp_0-18_S112
nb_sequences nb_clusters nb_samples
ASV denoising 32631 81 1
OTU after vsearch reclustering at 97% 32631 56 1
OTU vs after mumu cleaning algorithm 32631 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_0-34_S180
nb_sequences nb_clusters nb_samples
ASV denoising 32870 143 1
OTU after vsearch reclustering at 97% 32870 129 1
OTU vs after mumu cleaning algorithm 32870 119 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_0-50_S190
nb_sequences nb_clusters nb_samples
ASV denoising 31296 95 1
OTU after vsearch reclustering at 97% 31296 84 1
OTU vs after mumu cleaning algorithm 31296 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_001A_S145
nb_sequences nb_clusters nb_samples
ASV denoising 32509 133 1
OTU after vsearch reclustering at 97% 32509 115 1
OTU vs after mumu cleaning algorithm 32509 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_001B_S170
nb_sequences nb_clusters nb_samples
ASV denoising 44333 49 1
OTU after vsearch reclustering at 97% 44333 38 1
OTU vs after mumu cleaning algorithm 44333 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_001C_S98
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_002A_S104
nb_sequences nb_clusters nb_samples
ASV denoising 20956 51 1
OTU after vsearch reclustering at 97% 20956 42 1
OTU vs after mumu cleaning algorithm 20956 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_002B_S160
nb_sequences nb_clusters nb_samples
ASV denoising 34772 76 1
OTU after vsearch reclustering at 97% 34772 66 1
OTU vs after mumu cleaning algorithm 34772 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_002C_S139
nb_sequences nb_clusters nb_samples
ASV denoising 43814 115 1
OTU after vsearch reclustering at 97% 43814 98 1
OTU vs after mumu cleaning algorithm 43814 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 69 1
samp_003A_S115
nb_sequences nb_clusters nb_samples
ASV denoising 29108 84 1
OTU after vsearch reclustering at 97% 29108 64 1
OTU vs after mumu cleaning algorithm 29108 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_003C_S182
nb_sequences nb_clusters nb_samples
ASV denoising 33900 105 1
OTU after vsearch reclustering at 97% 33900 88 1
OTU vs after mumu cleaning algorithm 33900 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_004A_S167
nb_sequences nb_clusters nb_samples
ASV denoising 40335 68 1
OTU after vsearch reclustering at 97% 40335 41 1
OTU vs after mumu cleaning algorithm 40335 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_004B_S148
nb_sequences nb_clusters nb_samples
ASV denoising 30435 57 1
OTU after vsearch reclustering at 97% 30435 38 1
OTU vs after mumu cleaning algorithm 30435 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_004C_S138
nb_sequences nb_clusters nb_samples
ASV denoising 38056 92 1
OTU after vsearch reclustering at 97% 38056 73 1
OTU vs after mumu cleaning algorithm 38056 73 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_005A_S111
nb_sequences nb_clusters nb_samples
ASV denoising 36140 103 1
OTU after vsearch reclustering at 97% 36140 92 1
OTU vs after mumu cleaning algorithm 36140 83 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_005B_S200
nb_sequences nb_clusters nb_samples
ASV denoising 26521 67 1
OTU after vsearch reclustering at 97% 26521 58 1
OTU vs after mumu cleaning algorithm 26521 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_005C_S178
nb_sequences nb_clusters nb_samples
ASV denoising 36571 110 1
OTU after vsearch reclustering at 97% 36571 84 1
OTU vs after mumu cleaning algorithm 36571 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_006A_S128
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_006B_S116
nb_sequences nb_clusters nb_samples
ASV denoising 27642 166 1
OTU after vsearch reclustering at 97% 27642 149 1
OTU vs after mumu cleaning algorithm 27642 147 1
OTU vs + mumu + rarefaction by sequencing depth 2000 129 1
samp_006C_S156
nb_sequences nb_clusters nb_samples
ASV denoising 73 2 1
OTU after vsearch reclustering at 97% 73 2 1
OTU vs after mumu cleaning algorithm 73 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_007A_S130
nb_sequences nb_clusters nb_samples
ASV denoising 39349 65 1
OTU after vsearch reclustering at 97% 39349 49 1
OTU vs after mumu cleaning algorithm 39349 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_007B_S191
nb_sequences nb_clusters nb_samples
ASV denoising 33694 127 1
OTU after vsearch reclustering at 97% 33694 113 1
OTU vs after mumu cleaning algorithm 33694 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 99 1
samp_007C_S131
nb_sequences nb_clusters nb_samples
ASV denoising 39351 82 1
OTU after vsearch reclustering at 97% 39351 67 1
OTU vs after mumu cleaning algorithm 39351 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_008A_S153
nb_sequences nb_clusters nb_samples
ASV denoising 42550 75 1
OTU after vsearch reclustering at 97% 42550 45 1
OTU vs after mumu cleaning algorithm 42550 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_008A-PL2_S133
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_008C_S113
nb_sequences nb_clusters nb_samples
ASV denoising 28651 89 1
OTU after vsearch reclustering at 97% 28651 80 1
OTU vs after mumu cleaning algorithm 28651 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_009A_S134
nb_sequences nb_clusters nb_samples
ASV denoising 37520 121 1
OTU after vsearch reclustering at 97% 37520 103 1
OTU vs after mumu cleaning algorithm 37520 102 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_009B_S174
nb_sequences nb_clusters nb_samples
ASV denoising 478 3 1
OTU after vsearch reclustering at 97% 478 3 1
OTU vs after mumu cleaning algorithm 478 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_009B-PL2_S109
nb_sequences nb_clusters nb_samples
ASV denoising 32968 123 1
OTU after vsearch reclustering at 97% 32968 105 1
OTU vs after mumu cleaning algorithm 32968 105 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_009C_S105
nb_sequences nb_clusters nb_samples
ASV denoising 32 1 1
OTU after vsearch reclustering at 97% 32 1 1
OTU vs after mumu cleaning algorithm 32 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_010A_S189
nb_sequences nb_clusters nb_samples
ASV denoising 33074 116 1
OTU after vsearch reclustering at 97% 33074 91 1
OTU vs after mumu cleaning algorithm 33074 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_010B_S185
nb_sequences nb_clusters nb_samples
ASV denoising 33501 109 1
OTU after vsearch reclustering at 97% 33501 74 1
OTU vs after mumu cleaning algorithm 33501 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_010C_S197
nb_sequences nb_clusters nb_samples
ASV denoising 26265 79 1
OTU after vsearch reclustering at 97% 26265 73 1
OTU vs after mumu cleaning algorithm 26265 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_011A_S123
nb_sequences nb_clusters nb_samples
ASV denoising 48076 67 1
OTU after vsearch reclustering at 97% 48076 61 1
OTU vs after mumu cleaning algorithm 48076 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_011B_S121
nb_sequences nb_clusters nb_samples
ASV denoising 21388 70 1
OTU after vsearch reclustering at 97% 21388 58 1
OTU vs after mumu cleaning algorithm 21388 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_011C-PL2_S172
nb_sequences nb_clusters nb_samples
ASV denoising 31892 9 1
OTU after vsearch reclustering at 97% 31892 6 1
OTU vs after mumu cleaning algorithm 31892 6 1
OTU vs + mumu + rarefaction by sequencing depth 2000 6 1
samp_012A_S173
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_012B_S141
nb_sequences nb_clusters nb_samples
ASV denoising 31818 146 1
OTU after vsearch reclustering at 97% 31818 115 1
OTU vs after mumu cleaning algorithm 31818 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_012C_S126
nb_sequences nb_clusters nb_samples
ASV denoising 37039 59 1
OTU after vsearch reclustering at 97% 37039 53 1
OTU vs after mumu cleaning algorithm 37039 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_013A_S163
nb_sequences nb_clusters nb_samples
ASV denoising 33094 138 1
OTU after vsearch reclustering at 97% 33094 118 1
OTU vs after mumu cleaning algorithm 33094 116 1
OTU vs + mumu + rarefaction by sequencing depth 2000 102 1
samp_013B_S188
nb_sequences nb_clusters nb_samples
ASV denoising 41737 162 1
OTU after vsearch reclustering at 97% 41737 128 1
OTU vs after mumu cleaning algorithm 41737 123 1
OTU vs + mumu + rarefaction by sequencing depth 2000 104 1
samp_013D_S194
nb_sequences nb_clusters nb_samples
ASV denoising 27974 81 1
OTU after vsearch reclustering at 97% 27974 71 1
OTU vs after mumu cleaning algorithm 27974 71 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_014A_S196
nb_sequences nb_clusters nb_samples
ASV denoising 18158 89 1
OTU after vsearch reclustering at 97% 18158 86 1
OTU vs after mumu cleaning algorithm 18158 78 1
OTU vs + mumu + rarefaction by sequencing depth 2000 72 1
samp_014B_S154
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_014C_S114
nb_sequences nb_clusters nb_samples
ASV denoising 51598 85 1
OTU after vsearch reclustering at 97% 51598 70 1
OTU vs after mumu cleaning algorithm 51598 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_015A_S146
nb_sequences nb_clusters nb_samples
ASV denoising 34880 90 1
OTU after vsearch reclustering at 97% 34880 78 1
OTU vs after mumu cleaning algorithm 34880 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 63 1
samp_015C_S103
nb_sequences nb_clusters nb_samples
ASV denoising 33135 138 1
OTU after vsearch reclustering at 97% 33135 116 1
OTU vs after mumu cleaning algorithm 33135 116 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_016A_S119
nb_sequences nb_clusters nb_samples
ASV denoising 35668 139 1
OTU after vsearch reclustering at 97% 35668 128 1
OTU vs after mumu cleaning algorithm 35668 126 1
OTU vs + mumu + rarefaction by sequencing depth 2000 106 1
samp_016B_S176
nb_sequences nb_clusters nb_samples
ASV denoising 15084 85 1
OTU after vsearch reclustering at 97% 15084 75 1
OTU vs after mumu cleaning algorithm 15084 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_017A_S285
nb_sequences nb_clusters nb_samples
ASV denoising 20297 134 1
OTU after vsearch reclustering at 97% 20297 122 1
OTU vs after mumu cleaning algorithm 20297 118 1
OTU vs + mumu + rarefaction by sequencing depth 2000 109 1
samp_017B_S283
nb_sequences nb_clusters nb_samples
ASV denoising 28977 106 1
OTU after vsearch reclustering at 97% 28977 86 1
OTU vs after mumu cleaning algorithm 28977 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 74 1
samp_017C-PL2_S183
nb_sequences nb_clusters nb_samples
ASV denoising 30347 162 1
OTU after vsearch reclustering at 97% 30347 131 1
OTU vs after mumu cleaning algorithm 30347 121 1
OTU vs + mumu + rarefaction by sequencing depth 2000 106 1
samp_025A_S118
nb_sequences nb_clusters nb_samples
ASV denoising 19459 93 1
OTU after vsearch reclustering at 97% 19459 85 1
OTU vs after mumu cleaning algorithm 19459 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_037A_S151
nb_sequences nb_clusters nb_samples
ASV denoising 31 1 1
OTU after vsearch reclustering at 97% 31 1 1
OTU vs after mumu cleaning algorithm 31 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_11Aa_S265
nb_sequences nb_clusters nb_samples
ASV denoising 26320 89 1
OTU after vsearch reclustering at 97% 26320 83 1
OTU vs after mumu cleaning algorithm 26320 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_11Ab_S269
nb_sequences nb_clusters nb_samples
ASV denoising 24659 102 1
OTU after vsearch reclustering at 97% 24659 99 1
OTU vs after mumu cleaning algorithm 24659 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_11Ba_S291
nb_sequences nb_clusters nb_samples
ASV denoising 14794 69 1
OTU after vsearch reclustering at 97% 14794 58 1
OTU vs after mumu cleaning algorithm 14794 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_11Bb_S306
nb_sequences nb_clusters nb_samples
ASV denoising 8759 35 1
OTU after vsearch reclustering at 97% 8759 27 1
OTU vs after mumu cleaning algorithm 8759 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_11Ca_S272
nb_sequences nb_clusters nb_samples
ASV denoising 21061 109 1
OTU after vsearch reclustering at 97% 21061 105 1
OTU vs after mumu cleaning algorithm 21061 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_11Cb_S217
nb_sequences nb_clusters nb_samples
ASV denoising 20468 112 1
OTU after vsearch reclustering at 97% 20468 104 1
OTU vs after mumu cleaning algorithm 20468 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_11D_S62
nb_sequences nb_clusters nb_samples
ASV denoising 38792 138 1
OTU after vsearch reclustering at 97% 38792 120 1
OTU vs after mumu cleaning algorithm 38792 119 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_11Da_S300
nb_sequences nb_clusters nb_samples
ASV denoising 32604 149 1
OTU after vsearch reclustering at 97% 32604 130 1
OTU vs after mumu cleaning algorithm 32604 128 1
OTU vs + mumu + rarefaction by sequencing depth 2000 103 1
samp_11Da-PL4_S292
nb_sequences nb_clusters nb_samples
ASV denoising 30798 129 1
OTU after vsearch reclustering at 97% 30798 112 1
OTU vs after mumu cleaning algorithm 30798 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_11E_S19
nb_sequences nb_clusters nb_samples
ASV denoising 40710 150 1
OTU after vsearch reclustering at 97% 40710 128 1
OTU vs after mumu cleaning algorithm 40710 128 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_11Ea_S232
nb_sequences nb_clusters nb_samples
ASV denoising 33209 151 1
OTU after vsearch reclustering at 97% 33209 131 1
OTU vs after mumu cleaning algorithm 33209 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 108 1
samp_11Eb_S207
nb_sequences nb_clusters nb_samples
ASV denoising 25660 149 1
OTU after vsearch reclustering at 97% 25660 134 1
OTU vs after mumu cleaning algorithm 25660 133 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_11F_S54
nb_sequences nb_clusters nb_samples
ASV denoising 39375 82 1
OTU after vsearch reclustering at 97% 39375 70 1
OTU vs after mumu cleaning algorithm 39375 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_11Fa_S259
nb_sequences nb_clusters nb_samples
ASV denoising 27998 71 1
OTU after vsearch reclustering at 97% 27998 59 1
OTU vs after mumu cleaning algorithm 27998 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_11G_S32
nb_sequences nb_clusters nb_samples
ASV denoising 44141 82 1
OTU after vsearch reclustering at 97% 44141 68 1
OTU vs after mumu cleaning algorithm 44141 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_11Ga_S237
nb_sequences nb_clusters nb_samples
ASV denoising 40252 95 1
OTU after vsearch reclustering at 97% 40252 72 1
OTU vs after mumu cleaning algorithm 40252 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_11Gb_S236
nb_sequences nb_clusters nb_samples
ASV denoising 36217 85 1
OTU after vsearch reclustering at 97% 36217 67 1
OTU vs after mumu cleaning algorithm 36217 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_11H_S93
nb_sequences nb_clusters nb_samples
ASV denoising 41441 95 1
OTU after vsearch reclustering at 97% 41441 88 1
OTU vs after mumu cleaning algorithm 41441 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_11Ha_S310
nb_sequences nb_clusters nb_samples
ASV denoising 31275 81 1
OTU after vsearch reclustering at 97% 31275 78 1
OTU vs after mumu cleaning algorithm 31275 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_11Hb_S198
nb_sequences nb_clusters nb_samples
ASV denoising 28394 121 1
OTU after vsearch reclustering at 97% 28394 111 1
OTU vs after mumu cleaning algorithm 28394 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_11I_S166
nb_sequences nb_clusters nb_samples
ASV denoising 34063 86 1
OTU after vsearch reclustering at 97% 34063 63 1
OTU vs after mumu cleaning algorithm 34063 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_11Ia_S222
nb_sequences nb_clusters nb_samples
ASV denoising 22942 61 1
OTU after vsearch reclustering at 97% 22942 48 1
OTU vs after mumu cleaning algorithm 22942 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_11Ib_S225
nb_sequences nb_clusters nb_samples
ASV denoising 36015 83 1
OTU after vsearch reclustering at 97% 36015 59 1
OTU vs after mumu cleaning algorithm 36015 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_15B_S140
nb_sequences nb_clusters nb_samples
ASV denoising 19800 114 1
OTU after vsearch reclustering at 97% 19800 97 1
OTU vs after mumu cleaning algorithm 19800 90 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_16C_S168
nb_sequences nb_clusters nb_samples
ASV denoising 34088 124 1
OTU after vsearch reclustering at 97% 34088 99 1
OTU vs after mumu cleaning algorithm 34088 95 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_20A_S144
nb_sequences nb_clusters nb_samples
ASV denoising 31586 135 1
OTU after vsearch reclustering at 97% 31586 116 1
OTU vs after mumu cleaning algorithm 31586 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 92 1
samp_20Aa_S249
nb_sequences nb_clusters nb_samples
ASV denoising 27873 130 1
OTU after vsearch reclustering at 97% 27873 116 1
OTU vs after mumu cleaning algorithm 27873 114 1
OTU vs + mumu + rarefaction by sequencing depth 2000 100 1
samp_20Ab_S252
nb_sequences nb_clusters nb_samples
ASV denoising 43110 162 1
OTU after vsearch reclustering at 97% 43110 134 1
OTU vs after mumu cleaning algorithm 43110 126 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_20Ab-PL3_S241
nb_sequences nb_clusters nb_samples
ASV denoising 29717 73 1
OTU after vsearch reclustering at 97% 29717 43 1
OTU vs after mumu cleaning algorithm 29717 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_20B_S102
nb_sequences nb_clusters nb_samples
ASV denoising 31134 104 1
OTU after vsearch reclustering at 97% 31134 88 1
OTU vs after mumu cleaning algorithm 31134 88 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_20Ba_S278
nb_sequences nb_clusters nb_samples
ASV denoising 28681 89 1
OTU after vsearch reclustering at 97% 28681 80 1
OTU vs after mumu cleaning algorithm 28681 80 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_20Bb_S277
nb_sequences nb_clusters nb_samples
ASV denoising 25914 97 1
OTU after vsearch reclustering at 97% 25914 87 1
OTU vs after mumu cleaning algorithm 25914 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_20C_S49
nb_sequences nb_clusters nb_samples
ASV denoising 49371 118 1
OTU after vsearch reclustering at 97% 49371 99 1
OTU vs after mumu cleaning algorithm 49371 99 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_20Ca_S319
nb_sequences nb_clusters nb_samples
ASV denoising 27 1 1
OTU after vsearch reclustering at 97% 27 1 1
OTU vs after mumu cleaning algorithm 27 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Cb_S303
nb_sequences nb_clusters nb_samples
ASV denoising 38839 71 1
OTU after vsearch reclustering at 97% 38839 69 1
OTU vs after mumu cleaning algorithm 38839 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_20D_S82
nb_sequences nb_clusters nb_samples
ASV denoising 40735 158 1
OTU after vsearch reclustering at 97% 40735 131 1
OTU vs after mumu cleaning algorithm 40735 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 108 1
samp_20Da_S238
nb_sequences nb_clusters nb_samples
ASV denoising 1405 9 1
OTU after vsearch reclustering at 97% 1405 8 1
OTU vs after mumu cleaning algorithm 1405 8 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20E_S181
nb_sequences nb_clusters nb_samples
ASV denoising 37745 130 1
OTU after vsearch reclustering at 97% 37745 104 1
OTU vs after mumu cleaning algorithm 37745 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 89 1
samp_20Ea_S251
nb_sequences nb_clusters nb_samples
ASV denoising 31654 165 1
OTU after vsearch reclustering at 97% 31654 148 1
OTU vs after mumu cleaning algorithm 31654 144 1
OTU vs + mumu + rarefaction by sequencing depth 2000 128 1
samp_20Eb_S294
nb_sequences nb_clusters nb_samples
ASV denoising 27159 130 1
OTU after vsearch reclustering at 97% 27159 113 1
OTU vs after mumu cleaning algorithm 27159 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 99 1
samp_20F_S143
nb_sequences nb_clusters nb_samples
ASV denoising 35072 152 1
OTU after vsearch reclustering at 97% 35072 131 1
OTU vs after mumu cleaning algorithm 35072 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_20Fb_S214
nb_sequences nb_clusters nb_samples
ASV denoising 54 1 1
OTU after vsearch reclustering at 97% 54 1 1
OTU vs after mumu cleaning algorithm 54 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20G_S132
nb_sequences nb_clusters nb_samples
ASV denoising 38870 108 1
OTU after vsearch reclustering at 97% 38870 70 1
OTU vs after mumu cleaning algorithm 38870 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_20Ga_S220
nb_sequences nb_clusters nb_samples
ASV denoising 159 4 1
OTU after vsearch reclustering at 97% 159 4 1
OTU vs after mumu cleaning algorithm 159 4 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Ga2_S239
nb_sequences nb_clusters nb_samples
ASV denoising 26246 65 1
OTU after vsearch reclustering at 97% 26246 55 1
OTU vs after mumu cleaning algorithm 26246 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_20Gb_S284
nb_sequences nb_clusters nb_samples
ASV denoising 24298 97 1
OTU after vsearch reclustering at 97% 24298 74 1
OTU vs after mumu cleaning algorithm 24298 71 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_20H_S45
nb_sequences nb_clusters nb_samples
ASV denoising 43360 124 1
OTU after vsearch reclustering at 97% 43360 84 1
OTU vs after mumu cleaning algorithm 43360 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_20Ha_S219
nb_sequences nb_clusters nb_samples
ASV denoising 148 11 1
OTU after vsearch reclustering at 97% 148 11 1
OTU vs after mumu cleaning algorithm 148 11 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Hb_S230
nb_sequences nb_clusters nb_samples
ASV denoising 34057 143 1
OTU after vsearch reclustering at 97% 34057 107 1
OTU vs after mumu cleaning algorithm 34057 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_20I_S192
nb_sequences nb_clusters nb_samples
ASV denoising 39159 71 1
OTU after vsearch reclustering at 97% 39159 42 1
OTU vs after mumu cleaning algorithm 39159 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_20Ia_S224
nb_sequences nb_clusters nb_samples
ASV denoising 2197 10 1
OTU after vsearch reclustering at 97% 2197 9 1
OTU vs after mumu cleaning algorithm 2197 9 1
OTU vs + mumu + rarefaction by sequencing depth 2000 9 1
samp_20Ib_S289
nb_sequences nb_clusters nb_samples
ASV denoising 29987 63 1
OTU after vsearch reclustering at 97% 29987 35 1
OTU vs after mumu cleaning algorithm 29987 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_21A_S94
nb_sequences nb_clusters nb_samples
ASV denoising 35913 108 1
OTU after vsearch reclustering at 97% 35913 65 1
OTU vs after mumu cleaning algorithm 35913 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_21B_S7
nb_sequences nb_clusters nb_samples
ASV denoising 38573 79 1
OTU after vsearch reclustering at 97% 38573 58 1
OTU vs after mumu cleaning algorithm 38573 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_21Bb_S282
nb_sequences nb_clusters nb_samples
ASV denoising 28037 59 1
OTU after vsearch reclustering at 97% 28037 48 1
OTU vs after mumu cleaning algorithm 28037 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_21C_S77
nb_sequences nb_clusters nb_samples
ASV denoising 27592 120 1
OTU after vsearch reclustering at 97% 27592 117 1
OTU vs after mumu cleaning algorithm 27592 117 1
OTU vs + mumu + rarefaction by sequencing depth 2000 105 1
samp_21Ca_S246
nb_sequences nb_clusters nb_samples
ASV denoising 33801 144 1
OTU after vsearch reclustering at 97% 33801 134 1
OTU vs after mumu cleaning algorithm 33801 129 1
OTU vs + mumu + rarefaction by sequencing depth 2000 109 1
samp_21Cb_S276
nb_sequences nb_clusters nb_samples
ASV denoising 28543 125 1
OTU after vsearch reclustering at 97% 28543 115 1
OTU vs after mumu cleaning algorithm 28543 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_21D_S44
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21E_S47
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21eEb_S258
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21F_S48
nb_sequences nb_clusters nb_samples
ASV denoising 44927 14 1
OTU after vsearch reclustering at 97% 44927 10 1
OTU vs after mumu cleaning algorithm 44927 10 1
OTU vs + mumu + rarefaction by sequencing depth 2000 10 1
samp_21Fa_S253
nb_sequences nb_clusters nb_samples
ASV denoising 292 9 1
OTU after vsearch reclustering at 97% 292 9 1
OTU vs after mumu cleaning algorithm 292 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21G_S38
nb_sequences nb_clusters nb_samples
ASV denoising 32535 27 1
OTU after vsearch reclustering at 97% 32535 17 1
OTU vs after mumu cleaning algorithm 32535 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 16 1
samp_21Ga_S290
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21Gb_S296
nb_sequences nb_clusters nb_samples
ASV denoising 30146 26 1
OTU after vsearch reclustering at 97% 30146 15 1
OTU vs after mumu cleaning algorithm 30146 15 1
OTU vs + mumu + rarefaction by sequencing depth 2000 14 1
samp_21H_S68
nb_sequences nb_clusters nb_samples
ASV denoising 24269 69 1
OTU after vsearch reclustering at 97% 24269 63 1
OTU vs after mumu cleaning algorithm 24269 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_21Ha_S321
nb_sequences nb_clusters nb_samples
ASV denoising 28512 18 1
OTU after vsearch reclustering at 97% 28512 14 1
OTU vs after mumu cleaning algorithm 28512 14 1
OTU vs + mumu + rarefaction by sequencing depth 2000 14 1
samp_21HD_S195
nb_sequences nb_clusters nb_samples
ASV denoising 24793 75 1
OTU after vsearch reclustering at 97% 24793 70 1
OTU vs after mumu cleaning algorithm 24793 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_21I_S50
nb_sequences nb_clusters nb_samples
ASV denoising 39333 67 1
OTU after vsearch reclustering at 97% 39333 51 1
OTU vs after mumu cleaning algorithm 39333 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_21Ia_S233
nb_sequences nb_clusters nb_samples
ASV denoising 28102 64 1
OTU after vsearch reclustering at 97% 28102 55 1
OTU vs after mumu cleaning algorithm 28102 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_21Ib_S271
nb_sequences nb_clusters nb_samples
ASV denoising 28174 63 1
OTU after vsearch reclustering at 97% 28174 55 1
OTU vs after mumu cleaning algorithm 28174 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_22A_S15
nb_sequences nb_clusters nb_samples
ASV denoising 33895 121 1
OTU after vsearch reclustering at 97% 33895 91 1
OTU vs after mumu cleaning algorithm 33895 88 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_22D_S87
nb_sequences nb_clusters nb_samples
ASV denoising 30082 72 1
OTU after vsearch reclustering at 97% 30082 71 1
OTU vs after mumu cleaning algorithm 30082 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 63 1
samp_22E_S73
nb_sequences nb_clusters nb_samples
ASV denoising 40803 70 1
OTU after vsearch reclustering at 97% 40803 51 1
OTU vs after mumu cleaning algorithm 40803 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_22F_S60
nb_sequences nb_clusters nb_samples
ASV denoising 39874 131 1
OTU after vsearch reclustering at 97% 39874 116 1
OTU vs after mumu cleaning algorithm 39874 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 91 1
samp_23C_S84
nb_sequences nb_clusters nb_samples
ASV denoising 44643 146 1
OTU after vsearch reclustering at 97% 44643 133 1
OTU vs after mumu cleaning algorithm 44643 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_25B_S52
nb_sequences nb_clusters nb_samples
ASV denoising 37868 158 1
OTU after vsearch reclustering at 97% 37868 126 1
OTU vs after mumu cleaning algorithm 37868 122 1
OTU vs + mumu + rarefaction by sequencing depth 2000 99 1
samp_25C_S74
nb_sequences nb_clusters nb_samples
ASV denoising 48726 129 1
OTU after vsearch reclustering at 97% 48726 118 1
OTU vs after mumu cleaning algorithm 48726 115 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_25D_S76
nb_sequences nb_clusters nb_samples
ASV denoising 31545 55 1
OTU after vsearch reclustering at 97% 31545 44 1
OTU vs after mumu cleaning algorithm 31545 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_25E_S81
nb_sequences nb_clusters nb_samples
ASV denoising 25525 122 1
OTU after vsearch reclustering at 97% 25525 106 1
OTU vs after mumu cleaning algorithm 25525 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_25F_S67
nb_sequences nb_clusters nb_samples
ASV denoising 21 1 1
OTU after vsearch reclustering at 97% 21 1 1
OTU vs after mumu cleaning algorithm 21 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_26A_S83
nb_sequences nb_clusters nb_samples
ASV denoising 3826 45 1
OTU after vsearch reclustering at 97% 3826 45 1
OTU vs after mumu cleaning algorithm 3826 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_26B_S65
nb_sequences nb_clusters nb_samples
ASV denoising 37760 51 1
OTU after vsearch reclustering at 97% 37760 38 1
OTU vs after mumu cleaning algorithm 37760 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_26C_S8
nb_sequences nb_clusters nb_samples
ASV denoising 39588 65 1
OTU after vsearch reclustering at 97% 39588 42 1
OTU vs after mumu cleaning algorithm 39588 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_26D_S80
nb_sequences nb_clusters nb_samples
ASV denoising 37203 48 1
OTU after vsearch reclustering at 97% 37203 38 1
OTU vs after mumu cleaning algorithm 37203 37 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_26E_S135
nb_sequences nb_clusters nb_samples
ASV denoising 772 17 1
OTU after vsearch reclustering at 97% 772 17 1
OTU vs after mumu cleaning algorithm 772 17 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_26F_S66
nb_sequences nb_clusters nb_samples
ASV denoising 38529 63 1
OTU after vsearch reclustering at 97% 38529 41 1
OTU vs after mumu cleaning algorithm 38529 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_27A_S24
nb_sequences nb_clusters nb_samples
ASV denoising 38777 137 1
OTU after vsearch reclustering at 97% 38777 111 1
OTU vs after mumu cleaning algorithm 38777 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_27Aa_S235
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Ab_S293
nb_sequences nb_clusters nb_samples
ASV denoising 30071 155 1
OTU after vsearch reclustering at 97% 30071 139 1
OTU vs after mumu cleaning algorithm 30071 136 1
OTU vs + mumu + rarefaction by sequencing depth 2000 118 1
samp_27B_S17
nb_sequences nb_clusters nb_samples
ASV denoising 55777 70 1
OTU after vsearch reclustering at 97% 55777 45 1
OTU vs after mumu cleaning algorithm 55777 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_27Ba_S221
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Bb_S298
nb_sequences nb_clusters nb_samples
ASV denoising 29089 47 1
OTU after vsearch reclustering at 97% 29089 39 1
OTU vs after mumu cleaning algorithm 29089 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_27C_S53
nb_sequences nb_clusters nb_samples
ASV denoising 21045 85 1
OTU after vsearch reclustering at 97% 21045 68 1
OTU vs after mumu cleaning algorithm 21045 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_27Ca_S267
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Cb_S299
nb_sequences nb_clusters nb_samples
ASV denoising 1382 32 1
OTU after vsearch reclustering at 97% 1382 29 1
OTU vs after mumu cleaning algorithm 1382 27 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27D_S35
nb_sequences nb_clusters nb_samples
ASV denoising 64459 84 1
OTU after vsearch reclustering at 97% 64459 60 1
OTU vs after mumu cleaning algorithm 64459 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_27Db_S311
nb_sequences nb_clusters nb_samples
ASV denoising 36092 80 1
OTU after vsearch reclustering at 97% 36092 67 1
OTU vs after mumu cleaning algorithm 36092 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_27E_S89
nb_sequences nb_clusters nb_samples
ASV denoising 37924 128 1
OTU after vsearch reclustering at 97% 37924 105 1
OTU vs after mumu cleaning algorithm 37924 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_27Ea_S208
nb_sequences nb_clusters nb_samples
ASV denoising 32106 84 1
OTU after vsearch reclustering at 97% 32106 77 1
OTU vs after mumu cleaning algorithm 32106 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_27Eb_S312
nb_sequences nb_clusters nb_samples
ASV denoising 26940 104 1
OTU after vsearch reclustering at 97% 26940 89 1
OTU vs after mumu cleaning algorithm 26940 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_27F_S88
nb_sequences nb_clusters nb_samples
ASV denoising 33337 55 1
OTU after vsearch reclustering at 97% 33337 47 1
OTU vs after mumu cleaning algorithm 33337 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_27Fa_S256
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Fb_S288
nb_sequences nb_clusters nb_samples
ASV denoising 17375 51 1
OTU after vsearch reclustering at 97% 17375 42 1
OTU vs after mumu cleaning algorithm 17375 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_27G_S5
nb_sequences nb_clusters nb_samples
ASV denoising 47979 124 1
OTU after vsearch reclustering at 97% 47979 92 1
OTU vs after mumu cleaning algorithm 47979 92 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_27Ga_S240
nb_sequences nb_clusters nb_samples
ASV denoising 26 1 1
OTU after vsearch reclustering at 97% 26 1 1
OTU vs after mumu cleaning algorithm 26 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Gb_S242
nb_sequences nb_clusters nb_samples
ASV denoising 32556 100 1
OTU after vsearch reclustering at 97% 32556 81 1
OTU vs after mumu cleaning algorithm 32556 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_27H_S46
nb_sequences nb_clusters nb_samples
ASV denoising 43361 114 1
OTU after vsearch reclustering at 97% 43361 81 1
OTU vs after mumu cleaning algorithm 43361 80 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_27Ha_S287
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Hb_S280
nb_sequences nb_clusters nb_samples
ASV denoising 1 1 1
OTU after vsearch reclustering at 97% 1 1 1
OTU vs after mumu cleaning algorithm 1 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27I_S158
nb_sequences nb_clusters nb_samples
ASV denoising 33676 44 1
OTU after vsearch reclustering at 97% 33676 33 1
OTU vs after mumu cleaning algorithm 33676 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_27Ia_S245
nb_sequences nb_clusters nb_samples
ASV denoising 36653 65 1
OTU after vsearch reclustering at 97% 36653 53 1
OTU vs after mumu cleaning algorithm 36653 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_27Ib_S247
nb_sequences nb_clusters nb_samples
ASV denoising 30758 59 1
OTU after vsearch reclustering at 97% 30758 46 1
OTU vs after mumu cleaning algorithm 30758 45 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_28A_S9
nb_sequences nb_clusters nb_samples
ASV denoising 35935 76 1
OTU after vsearch reclustering at 97% 35935 49 1
OTU vs after mumu cleaning algorithm 35935 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_28B_S33
nb_sequences nb_clusters nb_samples
ASV denoising 26035 72 1
OTU after vsearch reclustering at 97% 26035 59 1
OTU vs after mumu cleaning algorithm 26035 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_28C_S31
nb_sequences nb_clusters nb_samples
ASV denoising 22155 45 1
OTU after vsearch reclustering at 97% 22155 35 1
OTU vs after mumu cleaning algorithm 22155 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_29A_S117
nb_sequences nb_clusters nb_samples
ASV denoising 42328 97 1
OTU after vsearch reclustering at 97% 42328 71 1
OTU vs after mumu cleaning algorithm 42328 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_29B_S187
nb_sequences nb_clusters nb_samples
ASV denoising 1033 24 1
OTU after vsearch reclustering at 97% 1033 23 1
OTU vs after mumu cleaning algorithm 1033 22 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_29C_S90
nb_sequences nb_clusters nb_samples
ASV denoising 40604 82 1
OTU after vsearch reclustering at 97% 40604 69 1
OTU vs after mumu cleaning algorithm 40604 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_29D_S71
nb_sequences nb_clusters nb_samples
ASV denoising 23180 89 1
OTU after vsearch reclustering at 97% 23180 62 1
OTU vs after mumu cleaning algorithm 23180 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_29F_S59
nb_sequences nb_clusters nb_samples
ASV denoising 46314 28 1
OTU after vsearch reclustering at 97% 46314 17 1
OTU vs after mumu cleaning algorithm 46314 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_29H1-50_S34
nb_sequences nb_clusters nb_samples
ASV denoising 27252 111 1
OTU after vsearch reclustering at 97% 27252 106 1
OTU vs after mumu cleaning algorithm 27252 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 86 1
samp_29H1-50-PL1_S3
nb_sequences nb_clusters nb_samples
ASV denoising 33420 81 1
OTU after vsearch reclustering at 97% 33420 62 1
OTU vs after mumu cleaning algorithm 33420 62 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_29I_S58
nb_sequences nb_clusters nb_samples
ASV denoising 35649 74 1
OTU after vsearch reclustering at 97% 35649 46 1
OTU vs after mumu cleaning algorithm 35649 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_29I1-50_S85
nb_sequences nb_clusters nb_samples
ASV denoising 42723 134 1
OTU after vsearch reclustering at 97% 42723 91 1
OTU vs after mumu cleaning algorithm 42723 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_29J_S40
nb_sequences nb_clusters nb_samples
ASV denoising 37596 85 1
OTU after vsearch reclustering at 97% 37596 50 1
OTU vs after mumu cleaning algorithm 37596 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_29K_S175
nb_sequences nb_clusters nb_samples
ASV denoising 41112 113 1
OTU after vsearch reclustering at 97% 41112 77 1
OTU vs after mumu cleaning algorithm 41112 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_29K-PL1_S26
nb_sequences nb_clusters nb_samples
ASV denoising 40718 86 1
OTU after vsearch reclustering at 97% 40718 50 1
OTU vs after mumu cleaning algorithm 40718 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_29L_S122
nb_sequences nb_clusters nb_samples
ASV denoising 46637 67 1
OTU after vsearch reclustering at 97% 46637 57 1
OTU vs after mumu cleaning algorithm 46637 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_31-32A_S155
nb_sequences nb_clusters nb_samples
ASV denoising 34 1 1
OTU after vsearch reclustering at 97% 34 1 1
OTU vs after mumu cleaning algorithm 34 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_31-32A-PL2_S101
nb_sequences nb_clusters nb_samples
ASV denoising 43301 88 1
OTU after vsearch reclustering at 97% 43301 66 1
OTU vs after mumu cleaning algorithm 43301 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_31-32B_S157
nb_sequences nb_clusters nb_samples
ASV denoising 39063 87 1
OTU after vsearch reclustering at 97% 39063 65 1
OTU vs after mumu cleaning algorithm 39063 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_31-32C_S137
nb_sequences nb_clusters nb_samples
ASV denoising 11583 39 1
OTU after vsearch reclustering at 97% 11583 27 1
OTU vs after mumu cleaning algorithm 11583 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_31-32E_S124
nb_sequences nb_clusters nb_samples
ASV denoising 35315 112 1
OTU after vsearch reclustering at 97% 35315 101 1
OTU vs after mumu cleaning algorithm 35315 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_31-32F_S199
nb_sequences nb_clusters nb_samples
ASV denoising 34203 56 1
OTU after vsearch reclustering at 97% 34203 36 1
OTU vs after mumu cleaning algorithm 34203 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_31A_S21
nb_sequences nb_clusters nb_samples
ASV denoising 33488 84 1
OTU after vsearch reclustering at 97% 33488 65 1
OTU vs after mumu cleaning algorithm 33488 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_31B_S79
nb_sequences nb_clusters nb_samples
ASV denoising 45605 38 1
OTU after vsearch reclustering at 97% 45605 34 1
OTU vs after mumu cleaning algorithm 45605 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_31C_S36
nb_sequences nb_clusters nb_samples
ASV denoising 38766 144 1
OTU after vsearch reclustering at 97% 38766 112 1
OTU vs after mumu cleaning algorithm 38766 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_32A_S95
nb_sequences nb_clusters nb_samples
ASV denoising 45194 113 1
OTU after vsearch reclustering at 97% 45194 70 1
OTU vs after mumu cleaning algorithm 45194 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_32B_S39
nb_sequences nb_clusters nb_samples
ASV denoising 627 17 1
OTU after vsearch reclustering at 97% 627 17 1
OTU vs after mumu cleaning algorithm 627 17 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_32C_S23
nb_sequences nb_clusters nb_samples
ASV denoising 56952 52 1
OTU after vsearch reclustering at 97% 56952 30 1
OTU vs after mumu cleaning algorithm 56952 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_33A_S179
nb_sequences nb_clusters nb_samples
ASV denoising 23291 7 1
OTU after vsearch reclustering at 97% 23291 4 1
OTU vs after mumu cleaning algorithm 23291 4 1
OTU vs + mumu + rarefaction by sequencing depth 2000 4 1
samp_33C_S136
nb_sequences nb_clusters nb_samples
ASV denoising 38854 125 1
OTU after vsearch reclustering at 97% 38854 113 1
OTU vs after mumu cleaning algorithm 38854 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_33C-PL2_S108
nb_sequences nb_clusters nb_samples
ASV denoising 20795 48 1
OTU after vsearch reclustering at 97% 20795 39 1
OTU vs after mumu cleaning algorithm 20795 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_35A_S1
nb_sequences nb_clusters nb_samples
ASV denoising 41587 66 1
OTU after vsearch reclustering at 97% 41587 43 1
OTU vs after mumu cleaning algorithm 41587 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_35ab27Da_S318
nb_sequences nb_clusters nb_samples
ASV denoising 28849 103 1
OTU after vsearch reclustering at 97% 28849 91 1
OTU vs after mumu cleaning algorithm 28849 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 74 1
samp_35B_S63
nb_sequences nb_clusters nb_samples
ASV denoising 30391 63 1
OTU after vsearch reclustering at 97% 30391 47 1
OTU vs after mumu cleaning algorithm 30391 45 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_35Ba_S301
nb_sequences nb_clusters nb_samples
ASV denoising 37124 101 1
OTU after vsearch reclustering at 97% 37124 84 1
OTU vs after mumu cleaning algorithm 37124 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_35Bb_S297
nb_sequences nb_clusters nb_samples
ASV denoising 35911 72 1
OTU after vsearch reclustering at 97% 35911 53 1
OTU vs after mumu cleaning algorithm 35911 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_35C_S4
nb_sequences nb_clusters nb_samples
ASV denoising 1673 15 1
OTU after vsearch reclustering at 97% 1673 14 1
OTU vs after mumu cleaning algorithm 1673 14 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_35Ca_S302
nb_sequences nb_clusters nb_samples
ASV denoising 51 1 1
OTU after vsearch reclustering at 97% 51 1 1
OTU vs after mumu cleaning algorithm 51 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_35Cb_S275
nb_sequences nb_clusters nb_samples
ASV denoising 20327 108 1
OTU after vsearch reclustering at 97% 20327 99 1
OTU vs after mumu cleaning algorithm 20327 99 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_35D_S165
nb_sequences nb_clusters nb_samples
ASV denoising 35959 86 1
OTU after vsearch reclustering at 97% 35959 52 1
OTU vs after mumu cleaning algorithm 35959 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_35Da_S227
nb_sequences nb_clusters nb_samples
ASV denoising 25858 72 1
OTU after vsearch reclustering at 97% 25858 48 1
OTU vs after mumu cleaning algorithm 25858 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_35Db_S315
nb_sequences nb_clusters nb_samples
ASV denoising 28317 66 1
OTU after vsearch reclustering at 97% 28317 40 1
OTU vs after mumu cleaning algorithm 28317 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_35Ea_S228
nb_sequences nb_clusters nb_samples
ASV denoising 20333 57 1
OTU after vsearch reclustering at 97% 20333 40 1
OTU vs after mumu cleaning algorithm 20333 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_35Eb_S216
nb_sequences nb_clusters nb_samples
ASV denoising 27796 63 1
OTU after vsearch reclustering at 97% 27796 38 1
OTU vs after mumu cleaning algorithm 27796 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_35Fa_S250
nb_sequences nb_clusters nb_samples
ASV denoising 39391 39 1
OTU after vsearch reclustering at 97% 39391 29 1
OTU vs after mumu cleaning algorithm 39391 29 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_35Fb_S244
nb_sequences nb_clusters nb_samples
ASV denoising 45036 50 1
OTU after vsearch reclustering at 97% 45036 32 1
OTU vs after mumu cleaning algorithm 45036 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_35G_S14
nb_sequences nb_clusters nb_samples
ASV denoising 39131 56 1
OTU after vsearch reclustering at 97% 39131 35 1
OTU vs after mumu cleaning algorithm 39131 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_35Ga_S314
nb_sequences nb_clusters nb_samples
ASV denoising 31428 65 1
OTU after vsearch reclustering at 97% 31428 57 1
OTU vs after mumu cleaning algorithm 31428 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_35Gb_S262
nb_sequences nb_clusters nb_samples
ASV denoising 32622 66 1
OTU after vsearch reclustering at 97% 32622 51 1
OTU vs after mumu cleaning algorithm 32622 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_35H_S162
nb_sequences nb_clusters nb_samples
ASV denoising 43714 59 1
OTU after vsearch reclustering at 97% 43714 46 1
OTU vs after mumu cleaning algorithm 43714 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_35Ha_S273
nb_sequences nb_clusters nb_samples
ASV denoising 27159 57 1
OTU after vsearch reclustering at 97% 27159 48 1
OTU vs after mumu cleaning algorithm 27159 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_35Hb_S248
nb_sequences nb_clusters nb_samples
ASV denoising 34346 73 1
OTU after vsearch reclustering at 97% 34346 51 1
OTU vs after mumu cleaning algorithm 34346 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_35Ia_S274
nb_sequences nb_clusters nb_samples
ASV denoising 28834 46 1
OTU after vsearch reclustering at 97% 28834 36 1
OTU vs after mumu cleaning algorithm 28834 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_35Ib_S234
nb_sequences nb_clusters nb_samples
ASV denoising 31094 32 1
OTU after vsearch reclustering at 97% 31094 23 1
OTU vs after mumu cleaning algorithm 31094 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_36A_S10
nb_sequences nb_clusters nb_samples
ASV denoising 48612 102 1
OTU after vsearch reclustering at 97% 48612 60 1
OTU vs after mumu cleaning algorithm 48612 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_36B_S28
nb_sequences nb_clusters nb_samples
ASV denoising 34759 64 1
OTU after vsearch reclustering at 97% 34759 54 1
OTU vs after mumu cleaning algorithm 34759 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_36B1-50_S41
nb_sequences nb_clusters nb_samples
ASV denoising 40558 82 1
OTU after vsearch reclustering at 97% 40558 62 1
OTU vs after mumu cleaning algorithm 40558 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_36C_S11
nb_sequences nb_clusters nb_samples
ASV denoising 179 9 1
OTU after vsearch reclustering at 97% 179 9 1
OTU vs after mumu cleaning algorithm 179 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_36D_S16
nb_sequences nb_clusters nb_samples
ASV denoising 36863 117 1
OTU after vsearch reclustering at 97% 36863 106 1
OTU vs after mumu cleaning algorithm 36863 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 85 1
samp_36E_S91
nb_sequences nb_clusters nb_samples
ASV denoising 78 2 1
OTU after vsearch reclustering at 97% 78 2 1
OTU vs after mumu cleaning algorithm 78 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_36F_S75
nb_sequences nb_clusters nb_samples
ASV denoising 314 6 1
OTU after vsearch reclustering at 97% 314 5 1
OTU vs after mumu cleaning algorithm 314 5 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_37B_S150
nb_sequences nb_clusters nb_samples
ASV denoising 23788 98 1
OTU after vsearch reclustering at 97% 23788 74 1
OTU vs after mumu cleaning algorithm 23788 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_37C_S125
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_37D_S100
nb_sequences nb_clusters nb_samples
ASV denoising 27320 100 1
OTU after vsearch reclustering at 97% 27320 80 1
OTU vs after mumu cleaning algorithm 27320 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_38A_S70
nb_sequences nb_clusters nb_samples
ASV denoising 48087 121 1
OTU after vsearch reclustering at 97% 48087 88 1
OTU vs after mumu cleaning algorithm 48087 85 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_38B_S18
nb_sequences nb_clusters nb_samples
ASV denoising 38946 72 1
OTU after vsearch reclustering at 97% 38946 52 1
OTU vs after mumu cleaning algorithm 38946 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_38C_S152
nb_sequences nb_clusters nb_samples
ASV denoising 26296 156 1
OTU after vsearch reclustering at 97% 26296 147 1
OTU vs after mumu cleaning algorithm 26296 144 1
OTU vs + mumu + rarefaction by sequencing depth 2000 114 1
samp_38D_S13
nb_sequences nb_clusters nb_samples
ASV denoising 36851 122 1
OTU after vsearch reclustering at 97% 36851 101 1
OTU vs after mumu cleaning algorithm 36851 98 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_39A_S51
nb_sequences nb_clusters nb_samples
ASV denoising 33352 50 1
OTU after vsearch reclustering at 97% 33352 38 1
OTU vs after mumu cleaning algorithm 33352 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_39B_S42
nb_sequences nb_clusters nb_samples
ASV denoising 67 2 1
OTU after vsearch reclustering at 97% 67 2 1
OTU vs after mumu cleaning algorithm 67 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_39C_S99
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_40A_S61
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_40B_S106
nb_sequences nb_clusters nb_samples
ASV denoising 39393 130 1
OTU after vsearch reclustering at 97% 39393 112 1
OTU vs after mumu cleaning algorithm 39393 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_40Bbis_S55
nb_sequences nb_clusters nb_samples
ASV denoising 20242 88 1
OTU after vsearch reclustering at 97% 20242 78 1
OTU vs after mumu cleaning algorithm 20242 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_40G_S29
nb_sequences nb_clusters nb_samples
ASV denoising 98 2 1
OTU after vsearch reclustering at 97% 98 2 1
OTU vs after mumu cleaning algorithm 98 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_41A_S22
nb_sequences nb_clusters nb_samples
ASV denoising 28716 64 1
OTU after vsearch reclustering at 97% 28716 49 1
OTU vs after mumu cleaning algorithm 28716 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_41C_S92
nb_sequences nb_clusters nb_samples
ASV denoising 19356 101 1
OTU after vsearch reclustering at 97% 19356 91 1
OTU vs after mumu cleaning algorithm 19356 90 1
OTU vs + mumu + rarefaction by sequencing depth 2000 72 1
samp_42A_S147
nb_sequences nb_clusters nb_samples
ASV denoising 40897 89 1
OTU after vsearch reclustering at 97% 40897 43 1
OTU vs after mumu cleaning algorithm 40897 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_42Aa_S309
nb_sequences nb_clusters nb_samples
ASV denoising 425 15 1
OTU after vsearch reclustering at 97% 425 15 1
OTU vs after mumu cleaning algorithm 425 15 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Aa-PL3_S226
nb_sequences nb_clusters nb_samples
ASV denoising 310 13 1
OTU after vsearch reclustering at 97% 310 13 1
OTU vs after mumu cleaning algorithm 310 13 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42B_S161
nb_sequences nb_clusters nb_samples
ASV denoising 1756 14 1
OTU after vsearch reclustering at 97% 1756 14 1
OTU vs after mumu cleaning algorithm 1756 14 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Ba_S270
nb_sequences nb_clusters nb_samples
ASV denoising 372 8 1
OTU after vsearch reclustering at 97% 372 8 1
OTU vs after mumu cleaning algorithm 372 8 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Bb_S305
nb_sequences nb_clusters nb_samples
ASV denoising 38495 56 1
OTU after vsearch reclustering at 97% 38495 40 1
OTU vs after mumu cleaning algorithm 38495 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_42C_S205
nb_sequences nb_clusters nb_samples
ASV denoising 510 9 1
OTU after vsearch reclustering at 97% 510 9 1
OTU vs after mumu cleaning algorithm 510 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Ca_S260
nb_sequences nb_clusters nb_samples
ASV denoising 48 1 1
OTU after vsearch reclustering at 97% 48 1 1
OTU vs after mumu cleaning algorithm 48 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42D_S127
nb_sequences nb_clusters nb_samples
ASV denoising 35635 84 1
OTU after vsearch reclustering at 97% 35635 65 1
OTU vs after mumu cleaning algorithm 35635 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_42Da_S307
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Db_S255
nb_sequences nb_clusters nb_samples
ASV denoising 36406 132 1
OTU after vsearch reclustering at 97% 36406 112 1
OTU vs after mumu cleaning algorithm 36406 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_42E_S171
nb_sequences nb_clusters nb_samples
ASV denoising 31804 86 1
OTU after vsearch reclustering at 97% 31804 63 1
OTU vs after mumu cleaning algorithm 31804 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_42Ea_S308
nb_sequences nb_clusters nb_samples
ASV denoising 7329 83 1
OTU after vsearch reclustering at 97% 7329 82 1
OTU vs after mumu cleaning algorithm 7329 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_42Eb_S263
nb_sequences nb_clusters nb_samples
ASV denoising 29413 149 1
OTU after vsearch reclustering at 97% 29413 130 1
OTU vs after mumu cleaning algorithm 29413 128 1
OTU vs + mumu + rarefaction by sequencing depth 2000 111 1
samp_42F_S129
nb_sequences nb_clusters nb_samples
ASV denoising 37829 94 1
OTU after vsearch reclustering at 97% 37829 88 1
OTU vs after mumu cleaning algorithm 37829 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 63 1
samp_42Fa_S266
nb_sequences nb_clusters nb_samples
ASV denoising 32192 112 1
OTU after vsearch reclustering at 97% 32192 106 1
OTU vs after mumu cleaning algorithm 32192 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_42Fb-PL3_S264
nb_sequences nb_clusters nb_samples
ASV denoising 25379 65 1
OTU after vsearch reclustering at 97% 25379 61 1
OTU vs after mumu cleaning algorithm 25379 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_42G_S107
nb_sequences nb_clusters nb_samples
ASV denoising 21661 40 1
OTU after vsearch reclustering at 97% 21661 33 1
OTU vs after mumu cleaning algorithm 21661 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_42Ga2_S254
nb_sequences nb_clusters nb_samples
ASV denoising 28621 118 1
OTU after vsearch reclustering at 97% 28621 105 1
OTU vs after mumu cleaning algorithm 28621 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_42Gb_S209
nb_sequences nb_clusters nb_samples
ASV denoising 9708 57 1
OTU after vsearch reclustering at 97% 9708 52 1
OTU vs after mumu cleaning algorithm 9708 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_42H_S186
nb_sequences nb_clusters nb_samples
ASV denoising 24791 61 1
OTU after vsearch reclustering at 97% 24791 51 1
OTU vs after mumu cleaning algorithm 24791 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_42Ha_S286
nb_sequences nb_clusters nb_samples
ASV denoising 26438 100 1
OTU after vsearch reclustering at 97% 26438 90 1
OTU vs after mumu cleaning algorithm 26438 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_42Hb_S268
nb_sequences nb_clusters nb_samples
ASV denoising 19922 96 1
OTU after vsearch reclustering at 97% 19922 90 1
OTU vs after mumu cleaning algorithm 19922 90 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_42I_S169
nb_sequences nb_clusters nb_samples
ASV denoising 39245 56 1
OTU after vsearch reclustering at 97% 39245 40 1
OTU vs after mumu cleaning algorithm 39245 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_42Ia_S223
nb_sequences nb_clusters nb_samples
ASV denoising 34537 45 1
OTU after vsearch reclustering at 97% 34537 32 1
OTU vs after mumu cleaning algorithm 34537 31 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_42Ib_S317
nb_sequences nb_clusters nb_samples
ASV denoising 34406 55 1
OTU after vsearch reclustering at 97% 34406 44 1
OTU vs after mumu cleaning algorithm 34406 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 37 1
samp_43A_S64
nb_sequences nb_clusters nb_samples
ASV denoising 147 4 1
OTU after vsearch reclustering at 97% 147 4 1
OTU vs after mumu cleaning algorithm 147 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43C_S149
nb_sequences nb_clusters nb_samples
ASV denoising 190 3 1
OTU after vsearch reclustering at 97% 190 3 1
OTU vs after mumu cleaning algorithm 190 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43D_S69
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43E_S142
nb_sequences nb_clusters nb_samples
ASV denoising 33326 183 1
OTU after vsearch reclustering at 97% 33326 163 1
OTU vs after mumu cleaning algorithm 33326 154 1
OTU vs + mumu + rarefaction by sequencing depth 2000 121 1
samp_43F_S177
nb_sequences nb_clusters nb_samples
ASV denoising 405 4 1
OTU after vsearch reclustering at 97% 405 4 1
OTU vs after mumu cleaning algorithm 405 4 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_44A_S193
nb_sequences nb_clusters nb_samples
ASV denoising 35078 82 1
OTU after vsearch reclustering at 97% 35078 58 1
OTU vs after mumu cleaning algorithm 35078 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_44C_S164
nb_sequences nb_clusters nb_samples
ASV denoising 45047 43 1
OTU after vsearch reclustering at 97% 45047 35 1
OTU vs after mumu cleaning algorithm 45047 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_45_S110
nb_sequences nb_clusters nb_samples
ASV denoising 26959 127 1
OTU after vsearch reclustering at 97% 26959 114 1
OTU vs after mumu cleaning algorithm 26959 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_46F_S202
nb_sequences nb_clusters nb_samples
ASV denoising 26852 80 1
OTU after vsearch reclustering at 97% 26852 50 1
OTU vs after mumu cleaning algorithm 26852 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_47A1-50_S20
nb_sequences nb_clusters nb_samples
ASV denoising 34130 79 1
OTU after vsearch reclustering at 97% 34130 65 1
OTU vs after mumu cleaning algorithm 34130 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_47D_S211
nb_sequences nb_clusters nb_samples
ASV denoising 30871 97 1
OTU after vsearch reclustering at 97% 30871 76 1
OTU vs after mumu cleaning algorithm 30871 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_47E_S218
nb_sequences nb_clusters nb_samples
ASV denoising 35555 99 1
OTU after vsearch reclustering at 97% 35555 78 1
OTU vs after mumu cleaning algorithm 35555 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_47F_S210
nb_sequences nb_clusters nb_samples
ASV denoising 22005 62 1
OTU after vsearch reclustering at 97% 22005 50 1
OTU vs after mumu cleaning algorithm 22005 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_47F-PL1_S6
nb_sequences nb_clusters nb_samples
ASV denoising 31344 96 1
OTU after vsearch reclustering at 97% 31344 74 1
OTU vs after mumu cleaning algorithm 31344 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_48a_S231
nb_sequences nb_clusters nb_samples
ASV denoising 41045 60 1
OTU after vsearch reclustering at 97% 41045 31 1
OTU vs after mumu cleaning algorithm 41045 31 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_48B_S215
nb_sequences nb_clusters nb_samples
ASV denoising 31011 81 1
OTU after vsearch reclustering at 97% 31011 56 1
OTU vs after mumu cleaning algorithm 31011 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_48C_S204
nb_sequences nb_clusters nb_samples
ASV denoising 34555 81 1
OTU after vsearch reclustering at 97% 34555 59 1
OTU vs after mumu cleaning algorithm 34555 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_48D_S201
nb_sequences nb_clusters nb_samples
ASV denoising 15814 58 1
OTU after vsearch reclustering at 97% 15814 54 1
OTU vs after mumu cleaning algorithm 15814 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_48E_S206
nb_sequences nb_clusters nb_samples
ASV denoising 26927 51 1
OTU after vsearch reclustering at 97% 26927 39 1
OTU vs after mumu cleaning algorithm 26927 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_48F_S203
nb_sequences nb_clusters nb_samples
ASV denoising 29791 78 1
OTU after vsearch reclustering at 97% 29791 57 1
OTU vs after mumu cleaning algorithm 29791 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_49A_S78
nb_sequences nb_clusters nb_samples
ASV denoising 38500 123 1
OTU after vsearch reclustering at 97% 38500 98 1
OTU vs after mumu cleaning algorithm 38500 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_49B_S2
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49B1-50_S27
nb_sequences nb_clusters nb_samples
ASV denoising 39646 133 1
OTU after vsearch reclustering at 97% 39646 100 1
OTU vs after mumu cleaning algorithm 39646 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_49C_S159
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49D_S86
nb_sequences nb_clusters nb_samples
ASV denoising 559 6 1
OTU after vsearch reclustering at 97% 559 5 1
OTU vs after mumu cleaning algorithm 559 5 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49E_S72
nb_sequences nb_clusters nb_samples
ASV denoising 43684 64 1
OTU after vsearch reclustering at 97% 43684 45 1
OTU vs after mumu cleaning algorithm 43684 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 36 1
samp_49F_S120
nb_sequences nb_clusters nb_samples
ASV denoising 28547 113 1
OTU after vsearch reclustering at 97% 28547 95 1
OTU vs after mumu cleaning algorithm 28547 85 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_52C_S57
nb_sequences nb_clusters nb_samples
ASV denoising 7786 50 1
OTU after vsearch reclustering at 97% 7786 47 1
OTU vs after mumu cleaning algorithm 7786 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_52D_S56
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_57S_S43
nb_sequences nb_clusters nb_samples
ASV denoising 38415 96 1
OTU after vsearch reclustering at 97% 38415 81 1
OTU vs after mumu cleaning algorithm 38415 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_B1_S30
nb_sequences nb_clusters nb_samples
ASV denoising 41258 71 1
OTU after vsearch reclustering at 97% 41258 57 1
OTU vs after mumu cleaning algorithm 41258 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_B3_S25
nb_sequences nb_clusters nb_samples
ASV denoising 37572 28 1
OTU after vsearch reclustering at 97% 37572 12 1
OTU vs after mumu cleaning algorithm 37572 12 1
OTU vs + mumu + rarefaction by sequencing depth 2000 12 1
samp_B4_S37
nb_sequences nb_clusters nb_samples
ASV denoising 30591 22 1
OTU after vsearch reclustering at 97% 30591 13 1
OTU vs after mumu cleaning algorithm 30591 13 1
OTU vs + mumu + rarefaction by sequencing depth 2000 13 1
samp_BI_S320
nb_sequences nb_clusters nb_samples
ASV denoising 31801 70 1
OTU after vsearch reclustering at 97% 31801 69 1
OTU vs after mumu cleaning algorithm 31801 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_Blanc_S212
nb_sequences nb_clusters nb_samples
ASV denoising 28671 11 1
OTU after vsearch reclustering at 97% 28671 10 1
OTU vs after mumu cleaning algorithm 28671 10 1
OTU vs + mumu + rarefaction by sequencing depth 2000 10 1
samp_Blnc35I-PL2_S184
nb_sequences nb_clusters nb_samples
ASV denoising 29268 10 1
OTU after vsearch reclustering at 97% 29268 5 1
OTU vs after mumu cleaning algorithm 29268 5 1
OTU vs + mumu + rarefaction by sequencing depth 2000 5 1
samp_GENSEQ1_S96
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_GENSEQ3_S281
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_GENSEQ5_S375
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_inconnus_S322
nb_sequences nb_clusters nb_samples
ASV denoising 393 1 1
OTU after vsearch reclustering at 97% 393 1 1
OTU vs after mumu cleaning algorithm 393 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL1-H12-35F_S324
nb_sequences nb_clusters nb_samples
ASV denoising 38771 60 1
OTU after vsearch reclustering at 97% 38771 40 1
OTU vs after mumu cleaning algorithm 38771 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_PL2-A1-33B_S325
nb_sequences nb_clusters nb_samples
ASV denoising 20571 83 1
OTU after vsearch reclustering at 97% 20571 77 1
OTU vs after mumu cleaning algorithm 20571 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_PL3-A12-35Aa_S326
nb_sequences nb_clusters nb_samples
ASV denoising 20729 63 1
OTU after vsearch reclustering at 97% 20729 59 1
OTU vs after mumu cleaning algorithm 20729 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_PL5-004a_S327
nb_sequences nb_clusters nb_samples
ASV denoising 17866 83 1
OTU after vsearch reclustering at 97% 17866 67 1
OTU vs after mumu cleaning algorithm 17866 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_PL5-004Ab_S328
nb_sequences nb_clusters nb_samples
ASV denoising 25067 111 1
OTU after vsearch reclustering at 97% 25067 88 1
OTU vs after mumu cleaning algorithm 25067 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 74 1
samp_PL5-004Ba_S329
nb_sequences nb_clusters nb_samples
ASV denoising 24545 63 1
OTU after vsearch reclustering at 97% 24545 41 1
OTU vs after mumu cleaning algorithm 24545 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 36 1
samp_PL5-004Cb_S332
nb_sequences nb_clusters nb_samples
ASV denoising 10928 43 1
OTU after vsearch reclustering at 97% 10928 38 1
OTU vs after mumu cleaning algorithm 10928 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 36 1
samp_PL5-005Aa_S333
nb_sequences nb_clusters nb_samples
ASV denoising 17903 96 1
OTU after vsearch reclustering at 97% 17903 86 1
OTU vs after mumu cleaning algorithm 17903 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_PL5-005Ba_S335
nb_sequences nb_clusters nb_samples
ASV denoising 33006 84 1
OTU after vsearch reclustering at 97% 33006 69 1
OTU vs after mumu cleaning algorithm 33006 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_PL5-005Bb_S334
nb_sequences nb_clusters nb_samples
ASV denoising 20 1 1
OTU after vsearch reclustering at 97% 20 1 1
OTU vs after mumu cleaning algorithm 20 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL5-005Ca_S336
nb_sequences nb_clusters nb_samples
ASV denoising 29219 99 1
OTU after vsearch reclustering at 97% 29219 94 1
OTU vs after mumu cleaning algorithm 29219 93 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_PL5-005Cb_S337
nb_sequences nb_clusters nb_samples
ASV denoising 28242 132 1
OTU after vsearch reclustering at 97% 28242 113 1
OTU vs after mumu cleaning algorithm 28242 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_PL5-006Aa_S338
nb_sequences nb_clusters nb_samples
ASV denoising 36782 145 1
OTU after vsearch reclustering at 97% 36782 125 1
OTU vs after mumu cleaning algorithm 36782 124 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_PL5-006Ab_S339
nb_sequences nb_clusters nb_samples
ASV denoising 20337 107 1
OTU after vsearch reclustering at 97% 20337 97 1
OTU vs after mumu cleaning algorithm 20337 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 88 1
samp_PL5-006Ba_S340
nb_sequences nb_clusters nb_samples
ASV denoising 27803 120 1
OTU after vsearch reclustering at 97% 27803 105 1
OTU vs after mumu cleaning algorithm 27803 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_PL5-006Bb_S341
nb_sequences nb_clusters nb_samples
ASV denoising 10514 88 1
OTU after vsearch reclustering at 97% 10514 81 1
OTU vs after mumu cleaning algorithm 10514 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_PL5-006Ca_S342
nb_sequences nb_clusters nb_samples
ASV denoising 26162 116 1
OTU after vsearch reclustering at 97% 26162 100 1
OTU vs after mumu cleaning algorithm 26162 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_PL5-006Cb_S343
nb_sequences nb_clusters nb_samples
ASV denoising 28422 112 1
OTU after vsearch reclustering at 97% 28422 101 1
OTU vs after mumu cleaning algorithm 28422 99 1
OTU vs + mumu + rarefaction by sequencing depth 2000 85 1
samp_PL5-024A_S348
nb_sequences nb_clusters nb_samples
ASV denoising 36430 99 1
OTU after vsearch reclustering at 97% 36430 80 1
OTU vs after mumu cleaning algorithm 36430 80 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_PL5-024B_S349
nb_sequences nb_clusters nb_samples
ASV denoising 21441 117 1
OTU after vsearch reclustering at 97% 21441 100 1
OTU vs after mumu cleaning algorithm 21441 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_PL5-024D_S351
nb_sequences nb_clusters nb_samples
ASV denoising 46352 138 1
OTU after vsearch reclustering at 97% 46352 108 1
OTU vs after mumu cleaning algorithm 46352 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_PL5-024E_S352
nb_sequences nb_clusters nb_samples
ASV denoising 32355 137 1
OTU after vsearch reclustering at 97% 32355 119 1
OTU vs after mumu cleaning algorithm 32355 118 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_PL5-21Aa_S344
nb_sequences nb_clusters nb_samples
ASV denoising 26052 124 1
OTU after vsearch reclustering at 97% 26052 114 1
OTU vs after mumu cleaning algorithm 26052 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_PL5-21Ab_S345
nb_sequences nb_clusters nb_samples
ASV denoising 30048 87 1
OTU after vsearch reclustering at 97% 30048 62 1
OTU vs after mumu cleaning algorithm 30048 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_PL5-21Ba_S346
nb_sequences nb_clusters nb_samples
ASV denoising 26292 68 1
OTU after vsearch reclustering at 97% 26292 52 1
OTU vs after mumu cleaning algorithm 26292 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_PL5-21Bb_S347
nb_sequences nb_clusters nb_samples
ASV denoising 35125 81 1
OTU after vsearch reclustering at 97% 35125 65 1
OTU vs after mumu cleaning algorithm 35125 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_PL5-24C_S350
nb_sequences nb_clusters nb_samples
ASV denoising 33655 94 1
OTU after vsearch reclustering at 97% 33655 79 1
OTU vs after mumu cleaning algorithm 33655 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_PL5-24F_S353
nb_sequences nb_clusters nb_samples
ASV denoising 31613 104 1
OTU after vsearch reclustering at 97% 31613 82 1
OTU vs after mumu cleaning algorithm 31613 78 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_PL5-24G_S354
nb_sequences nb_clusters nb_samples
ASV denoising 32954 86 1
OTU after vsearch reclustering at 97% 32954 64 1
OTU vs after mumu cleaning algorithm 32954 62 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_PL5-24H_S355
nb_sequences nb_clusters nb_samples
ASV denoising 26939 107 1
OTU after vsearch reclustering at 97% 26939 99 1
OTU vs after mumu cleaning algorithm 26939 98 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_PL5-24J_S356
nb_sequences nb_clusters nb_samples
ASV denoising 22255 39 1
OTU after vsearch reclustering at 97% 22255 34 1
OTU vs after mumu cleaning algorithm 22255 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_PL5-35I_S357
nb_sequences nb_clusters nb_samples
ASV denoising 27134 164 1
OTU after vsearch reclustering at 97% 27134 148 1
OTU vs after mumu cleaning algorithm 27134 144 1
OTU vs + mumu + rarefaction by sequencing depth 2000 131 1
samp_PL5-36A_S358
nb_sequences nb_clusters nb_samples
ASV denoising 41148 56 1
OTU after vsearch reclustering at 97% 41148 38 1
OTU vs after mumu cleaning algorithm 41148 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_PL5-42E_S359
nb_sequences nb_clusters nb_samples
ASV denoising 28303 100 1
OTU after vsearch reclustering at 97% 28303 67 1
OTU vs after mumu cleaning algorithm 28303 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_PL5-43B_S360
nb_sequences nb_clusters nb_samples
ASV denoising 28161 139 1
OTU after vsearch reclustering at 97% 28161 117 1
OTU vs after mumu cleaning algorithm 28161 114 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_PL5-44B_S361
nb_sequences nb_clusters nb_samples
ASV denoising 35302 106 1
OTU after vsearch reclustering at 97% 35302 98 1
OTU vs after mumu cleaning algorithm 35302 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_PL5-46A_S362
nb_sequences nb_clusters nb_samples
ASV denoising 32906 125 1
OTU after vsearch reclustering at 97% 32906 115 1
OTU vs after mumu cleaning algorithm 32906 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_PL5-46B_S363
nb_sequences nb_clusters nb_samples
ASV denoising 27938 67 1
OTU after vsearch reclustering at 97% 27938 50 1
OTU vs after mumu cleaning algorithm 27938 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_PL5-46D_S365
nb_sequences nb_clusters nb_samples
ASV denoising 30310 58 1
OTU after vsearch reclustering at 97% 30310 34 1
OTU vs after mumu cleaning algorithm 30310 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_PL5-46E_S366
nb_sequences nb_clusters nb_samples
ASV denoising 37112 68 1
OTU after vsearch reclustering at 97% 37112 48 1
OTU vs after mumu cleaning algorithm 37112 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_PL5-47A_S367
nb_sequences nb_clusters nb_samples
ASV denoising 32828 103 1
OTU after vsearch reclustering at 97% 32828 91 1
OTU vs after mumu cleaning algorithm 32828 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 74 1
samp_PL5-47B_S368
nb_sequences nb_clusters nb_samples
ASV denoising 26190 71 1
OTU after vsearch reclustering at 97% 26190 48 1
OTU vs after mumu cleaning algorithm 26190 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_PL5-47C_S369
nb_sequences nb_clusters nb_samples
ASV denoising 19259 51 1
OTU after vsearch reclustering at 97% 19259 44 1
OTU vs after mumu cleaning algorithm 19259 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_PL5-50_S370
nb_sequences nb_clusters nb_samples
ASV denoising 27851 80 1
OTU after vsearch reclustering at 97% 27851 75 1
OTU vs after mumu cleaning algorithm 27851 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_PL5-53_S371
nb_sequences nb_clusters nb_samples
ASV denoising 17139 67 1
OTU after vsearch reclustering at 97% 17139 59 1
OTU vs after mumu cleaning algorithm 17139 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_PL5-eau_S374
nb_sequences nb_clusters nb_samples
ASV denoising 0 10281 1
OTU after vsearch reclustering at 97% 0 4521 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL5-ENC024A_S373
nb_sequences nb_clusters nb_samples
ASV denoising 31627 153 1
OTU after vsearch reclustering at 97% 31627 127 1
OTU vs after mumu cleaning algorithm 31627 125 1
OTU vs + mumu + rarefaction by sequencing depth 2000 101 1
samp_PL5-ENC024C_S372
nb_sequences nb_clusters nb_samples
ASV denoising 19447 133 1
OTU after vsearch reclustering at 97% 19447 125 1
OTU vs after mumu cleaning algorithm 19447 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_Undetermined_S0
nb_sequences nb_clusters nb_samples
ASV denoising 95573 511 1
OTU after vsearch reclustering at 97% 95573 480 1
OTU vs after mumu cleaning algorithm 95573 480 1
OTU vs + mumu + rarefaction by sequencing depth 2000 344 1

Make krona html files

Code 
krona(clean_pq(d_pq, simplify_taxo =TRUE), file = here::here("data/data_final/krona_nb_seq.html"))
Cleaning suppress 0 taxa and 26 samples.
Code 
krona(clean_pq(d_pq, simplify_taxo =TRUE), nb_seq = FALSE, file =  here::here("data/data_final/krona_nb_taxa.html"))
Cleaning suppress 0 taxa and 26 samples.

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .

Code 
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] MiscMetabar_0.10.1 purrr_1.0.2        dplyr_1.1.4        dada2_1.34.0      
[5] Rcpp_1.0.13-1      ggplot2_3.5.1      phyloseq_1.50.0    targets_1.9.0     
[9] knitr_1.49        

loaded via a namespace (and not attached):
  [1] bitops_1.0-9                deldir_2.0-4               
  [3] permute_0.9-7               rlang_1.1.4                
  [5] magrittr_2.0.3              ade4_1.7-22                
  [7] matrixStats_1.4.1           compiler_4.4.2             
  [9] mgcv_1.9-1                  png_0.1-8                  
 [11] callr_3.7.6                 vctrs_0.6.5                
 [13] reshape2_1.4.4              autometric_0.1.2           
 [15] stringr_1.5.1               pwalign_1.2.0              
 [17] pkgconfig_2.0.3             crayon_1.5.3               
 [19] fastmap_1.2.0               backports_1.5.0            
 [21] XVector_0.46.0              labeling_0.4.3             
 [23] utf8_1.2.4                  Rsamtools_2.22.0           
 [25] rmarkdown_2.29              UCSC.utils_1.2.0           
 [27] ps_1.8.1                    xfun_0.49                  
 [29] cachem_1.1.0                zlibbioc_1.52.0            
 [31] GenomeInfoDb_1.42.1         jsonlite_1.8.9             
 [33] biomformat_1.34.0           rhdf5filters_1.18.0        
 [35] DelayedArray_0.32.0         Rhdf5lib_1.28.0            
 [37] BiocParallel_1.40.0         jpeg_0.1-10                
 [39] parallel_4.4.2              cluster_2.1.6              
 [41] R6_2.5.1                    bslib_0.8.0                
 [43] RColorBrewer_1.1-3          stringi_1.8.4              
 [45] jquerylib_0.1.4             GenomicRanges_1.58.0       
 [47] SummarizedExperiment_1.36.0 iterators_1.0.14           
 [49] IRanges_2.40.0              Matrix_1.7-1               
 [51] splines_4.4.2               igraph_2.1.1               
 [53] tidyselect_1.2.1            rstudioapi_0.17.1          
 [55] abind_1.4-8                 yaml_2.3.10                
 [57] vegan_2.6-8                 codetools_0.2-20           
 [59] hwriter_1.3.2.1             processx_3.8.4             
 [61] lattice_0.22-6              tibble_3.2.1               
 [63] plyr_1.8.9                  Biobase_2.66.0             
 [65] withr_3.0.2                 ShortRead_1.64.0           
 [67] evaluate_1.0.1              survival_3.7-0             
 [69] RcppParallel_5.1.9          Biostrings_2.74.0          
 [71] pillar_1.9.0                BiocManager_1.30.25        
 [73] MatrixGenerics_1.18.0       DT_0.33                    
 [75] renv_1.0.11                 foreach_1.5.2              
 [77] stats4_4.4.2                generics_0.1.3             
 [79] rprojroot_2.0.4             S4Vectors_0.44.0           
 [81] munsell_0.5.1               scales_1.3.0               
 [83] base64url_1.4               glue_1.8.0                 
 [85] tools_4.4.2                 interp_1.1-6               
 [87] data.table_1.16.2           GenomicAlignments_1.42.0   
 [89] visNetwork_2.1.2            rhdf5_2.50.0               
 [91] grid_4.4.2                  ape_5.8                    
 [93] crosstalk_1.2.1             latticeExtra_0.6-30        
 [95] colorspace_2.1-1            nlme_3.1-166               
 [97] GenomeInfoDbData_1.2.13     cli_3.6.3                  
 [99] fansi_1.0.6                 viridisLite_0.4.2          
[101] S4Arrays_1.6.0              gtable_0.3.6               
[103] sass_0.4.9                  digest_0.6.37              
[105] BiocGenerics_0.52.0         SparseArray_1.6.0          
[107] farver_2.1.2                htmlwidgets_1.6.4          
[109] htmltools_0.5.8.1           multtest_2.62.0            
[111] lifecycle_1.0.4             here_1.0.1                 
[113] httr_1.4.7                  secretbase_1.0.3           
[115] MASS_7.3-61

Citation

BibTeX citation:
@online{taudière2024,
  author = {Taudière, Adrien},
  title = {Bioinformatics Pipeline Summary},
  date = {2024-12-03},
  langid = {en}
}
For attribution, please cite this work as:
Taudière, Adrien. 2024. “Bioinformatics Pipeline Summary.” December 3, 2024.

This document was made by the Adrien Taudière, whith multiple inspirations from the Lumo quarto template.